BIOS 214 · Autumn 2026 · Stanford School of Medicine
Open-Source MRI Sequence Development: Simulation to Scanner
Taught by Carlos Castillo-Passi and Daniel Ennis
Hands-on MRI sequence design, simulation, acquisition, and reconstruction with open-source tools.
Overview
This interdisciplinary mini-course introduces an end-to-end workflow for rapid MRI sequence development and image reconstruction using open-source tools. Students will design pulse sequences in Pulseq, simulate and validate them with KomaMRI, and reconstruct simulated or acquired MRI data using BART and MRIReco. Students will also learn how Pulseq sequences and reconstruction workflows can be integrated directly on MRI scanners through Pulseq interpreters and OpenRecon.
The course combines short lectures with hands-on coding and lab sessions focused on rapid prototyping, simulation, acquisition, and reconstruction. It emphasizes research rigor, reproducibility, and transparency through open-source tools and reproducible workflows.
Intended for students with basic programming experience and an interest in MRI and computational methods.
Grading: MED S/NC (Satisfactory/No Credit).
Learning goals
By the end of this mini-course, students will be able to:
- Design basic MRI pulse sequences using Pulseq.
- Simulate MRI experiments using Bloch simulations in KomaMRI.
- Reconstruct MRI data using BART and MRIReco.
- Analyze the impact of sequence parameters on image contrast and artifacts.
- Implement and iterate on sequence designs using a rapid prototyping workflow.
- Evaluate sequence performance through simulation and scanner experiments.
Schedule & materials
| Week | Monday | Wednesday | Friday |
|---|---|---|---|
| Week 1 | Nov 9* Lecture: Coming soon Lab: Coming soon |
Nov 11 Lecture: Coming soon Lab: Coming soon |
Nov 13* Lecture: Coming soon Lab: Coming soon |
| Week 2 | Nov 16 Lecture: Coming soon Lab: Coming soon |
Nov 18 Lecture: Coming soon Lab: Coming soon |
Nov 20 Lecture: Coming soon Lab: Coming soon |
| Week 3 |  Thanksgiving break |
||
| Week 4 | Nov 30 Lecture: Coming soon Lab: Coming soon |
Dec 2 Lecture: Coming soon Lab: Coming soon |
Dec 4 Lecture: Coming soon Lab: Coming soon |
Classroom: 
CCSR4107. *November 9 and 13: M218/218A.
Lecture: 9:30–10:20 a.m.
Lab: 10:30–11:50 a.m.
Friday scanning: After the lecture, we’ll head to Cima.X (3T3) in the Lucas Center.
Lab setup
Before the first lab, please have:
- Julia 1.12 installed.
- A coding agent installed and ready to use, such as Codex or Claude Code. Complete its sign-in or account setup beforehand.
Canvas
Enrolled students can access BIOS 214 on Canvas for announcements, submissions, grades, and any restricted material.